2MME

Hybrid structure of the Shigella flexneri MxiH Type three secretion system needle

Experimental Data Snapshot

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 5000 
  • Conformers Submitted: 10 
  • Selection Criteria: target function 
  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.70 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy.

Demers, J.P., Habenstein, B., Loquet, A., Kumar Vasa, S., Giller, K., Becker, S., Baker, D., Lange, A., Sgourakis, N.G.

(2014) Nat Commun 5: 4976-4976

  • DOI: 10.1038/ncomms5976
  • Primary Citation of Related Structures:  
    2MME

  • PubMed Abstract: 

    • We introduce a general hybrid approach for determining the structures of supramolecular assemblies. Cryo-electron microscopy (cryo-EM) data define the overall envelope of the assembly and rigid-body orientation of the subunits while solid-state nuclear magnetic resonance (ssNMR) chemical shifts and distance constraints define the local secondary structure, protein fold and inter-subunit interactions ...

    We introduce a general hybrid approach for determining the structures of supramolecular assemblies. Cryo-electron microscopy (cryo-EM) data define the overall envelope of the assembly and rigid-body orientation of the subunits while solid-state nuclear magnetic resonance (ssNMR) chemical shifts and distance constraints define the local secondary structure, protein fold and inter-subunit interactions. Finally, Rosetta structure calculations provide a general framework to integrate the different sources of structural information. Combining a 7.7-Å cryo-EM density map and 996 ssNMR distance constraints, the structure of the type-III secretion system needle of Shigella flexneri is determined to a precision of 0.4 Å. The calculated structures are cross-validated using an independent data set of 691 ssNMR constraints and scanning transmission electron microscopy measurements. The hybrid model resolves the conformation of the non-conserved N terminus, which occupies a protrusion in the cryo-EM density, and reveals conserved pore residues forming a continuous pattern of electrostatic interactions, thereby suggesting a mechanism for effector protein translocation.

    Related Citations: 
    • Structure of a type III secretion needle at 7- angstrom resolution provides insights into its assembly and signaling mechanisms.
      Fujii, T., Cheung, M., Blanco, A., Kato, T., Blocker, A.J., Namba, K.
      (2012) Proc Natl Acad Sci U S A 109: 4461
    Organizational Affiliation: 

    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MxiH
A,
B,
C,
D,
E,
85Shigella flexneriMutation(s): 0 
Gene Names: mxiH
UniProt
Find proteins for Q6XVY0 (Shigella flexneri)
Explore Q6XVY0 
Go to UniProtKB:  Q6XVY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XVY0
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLID-STATE NMR
  • Conformers Calculated: 5000 
  • Conformers Submitted: 10 
  • Selection Criteria: target function 
  • OLDERADO: 2MME Olderado
  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.70 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Author supporting evidence, Data collection, Database references, Other